Assayer
A curated catalogue of 3,973 tools for medicinal and computational chemistry, paired with 27 actionable protocols guiding step-by-step drug discovery workflows, target validation against UniProt, and real-time PDB structure prioritization.
Sep 13, 2026
Choosing the Right Partial Charges for Molecular Docking: AM1-BCC, PM6 and Beyond
Partial charges quietly drive the electrostatics behind every docking score. This guide compares the common semi-empirical options - AM1-BCC, PM6, AM1/PM3, Gasteiger and RESP - and gives a practical recommendation for when to use each.
Feb 4, 2025
Understanding Binding Energetics in Molecular Docking
Conceptual overview of the key energetic contributions governing protein–ligand binding in molecular docking, including desolvation, entropy, water displacement, electrostatics, and scoring function behavior.
Jun 16, 2024
Practical System Preparation Tips for Molecular Dynamics Simulations
Practical choices that change MD results before the simulation starts: solvent box shape, protein termini, and how to pick a representative conformation.
May 21, 2024
Awesome Drug Discovery
A curated resource list of computational methods for drug discovery, covering molecular modeling tools, machine learning frameworks, databases, and open-source pipelines organized by application area.
Jan 16, 2024
Energy Minimization with Open Babel: Practical Guide for Ligand Preparation
Step-by-step workflow for energy minimization of ligands using Open Babel’s obminimize tool, with comparisons of force fields and minimization algorithms for docking and molecular modeling.
Jan 12, 2024
Principal Component Analysis and Free Energy Landscape Mapping Using GROMACS
Step-by-step workflow for performing PCA and Free Energy Landscape (FEL) analysis from MD simulations with GROMACS.
Nov 22, 2023
Validating Molecular Docking Poses with DFT: A Quick Guide
Learn how to use Density Functional Theory (DFT) to validate docking poses, estimate strain energies, and gain quantum insights into ligand binding.
Oct 27, 2023
Step-by-Step MD Simulation of a Protein–Ligand Complex with GROMACS
A clear workflow for setting up, running, and analyzing a protein–ligand complex simulation using CHARMM36 and TIP3P in GROMACS.
Sep 5, 2023
Molecular Simulation in Drug Discovery: A Strategic Guide to Core Methods
Overview of key molecular simulation methods (QM, MD, CGMD, MC, BD, LD, DPD) and their strategic applications in drug discovery pipelines.
Aug 10, 2023